Thanks Steve. I have raised complaint to the admin about this issue.

On Thu, May 11, 2023, 11:18 PM Steven R. Brandt <sbrandt@cct.lsu.edu> wrote:

I would talk to the system administrators about that. There is definitely something wrong with your compiler install if you can't find math.h.

--Steve

On 5/11/2023 2:02 AM, Shamim Haque 1910511 wrote:
Dear Steve,

I just rechecked the cpp program to output M_PI in the computing nodes, and that is not working right now, which was somehow working fine a few days ago. I also tried different gcc versions (4.8, 10.2, 11.1, gnu8/8.3) available in the cluster. All report similar issue:

prog.cpp:1:18: fatal error: math.h: No such file or directory
 #include <math.h>
                  ^
compilation terminated.

----OR-----

/home/apps/gcc-10.2.0/include/c++/10.2.0/x86_64-pc-linux-gnu/bits/os_defines.h:39:10: fatal error: features.h: No such file or directory
   39 | #include <features.h>
      |          ^~~~~~~~~~~~
compilation terminated. 

The cpp code seems to work fine in login node, as it gives out the value of pi upon execution. I am contacting the hpc admin to resolve this issue.

I am attaching the test code (prog.cpp), the sbatch jobscript (prog.sh) and the output file (slurn-117473.out), if you would like to have a look at it. 

Please let me know if I should try something different to get this working.

Regards
Shamim Haque
Senior Research Fellow (SRF)
Department of Physics
IISER Bhopal

ᐧ

On Mon, May 8, 2023 at 7:25 PM Shamim Haque 1910511 <shamims@iiserb.ac.in> wrote:
Thanks Steve. I'll make the changes and try again. I'll let you know the outcome.

Regards
Shamim Haque
Senior Research Fellow (SRF)
Department of Physics
IISER Bhopal

ᐧ

On Mon, May 8, 2023 at 7:21 PM Steven R. Brandt <sbrandt@cct.lsu.edu> wrote:

That tends to make me think you aren't using the compiler you think you're using. You could put full paths in the .cfg files and recompile from scratch.

i.e.

CXX = /full/path/to/icc

--Steve

On 5/3/2023 3:26 PM, Shamim Haque 1910511 wrote:
Yes, this gives the value of Pi successfully, before starting the compilation:

/home/vkerni.iitr/sam/trial
3.141593
Current machine: paramganga3
Using configuration: sim
Reconfiguring sim
Writing configuration to: /home/vkerni.iitr/sam/ET_debug/Cactus/configs/sim/OptionList
Cactus - version: 4.12.0
Reconfiguring sim.
.
.
.
checking for M_PI... no
configure: error: M_PI not defined. Try adding -D_XOPEN_SOURCE to CPPFLAGS.

Error reconfiguring sim-config
make: *** [sim-config] Error 2


Shamim Haque
Senior Research Fellow (SRF)
Department of Physics
IISER Bhopal

ᐧ

On Thu, May 4, 2023 at 12:29 AM Steven Brandt <sbrandt@cct.lsu.edu> wrote:

So, sanity check, can you compile the following program outside of Cactus?

#include <math.h>
#include <stdio.h>

int main() {
    printf("%f\n", M_PI);
    return 0;
}

On 5/3/2023 1:50 PM, Shamim Haque 1910511 wrote:
Dear Steve,

I tried gcc (10 and 11) as well and I am stuck with the following error:
configure: error: M_PI not defined. Try adding -D_XOPEN_SOURCE to CPPFLAGS.

This also happened for Intel (2020 and 2019). I have attached both the output files here. 

Please ignore the out file in the first email, I have uploaded another out file by mistake. The rest of the files are correct in the first mail.

Regards
Shamim Haque
Senior Research Fellow (SRF)
Department of Physics
IISER Bhopal

ᐧ

On Wed, May 3, 2023 at 8:04 PM Steven Brandt <sbrandt@cct.lsu.edu> wrote:

I notice from the output that your compiler claims "limits.h" is missing. Possibly there's something wrong with your icc setup? Maybe you should try using gcc / gfortran instead.

--Steve

On 5/3/2023 8:20 AM, Shamim Haque 1910511 wrote:
Dear Frank,

I added the alias pattern for the computing nodes and now ETK can detect the cluster (checked by asking "whoami") during the batch queuing. I'll get in touch with the admins to include 'patch'.

However, the problem still persists, having assured that the correct machine file and option list are being used during the compilation.

Regards
Shamim Haque
Senior Research Fellow (SRF)
Department of Physics
IISER Bhopal

ᐧ

On Wed, May 3, 2023 at 3:49 PM Frank Loeffler <frank.loeffler@uni-jena.de> wrote:
Hi Shamim

On Wed, May 03, 2023 at 03:11:49PM +0530, Shamim Haque 1910511 wrote:
>We are trying to compile ETK on ParamGanga at IIT Roorkee. The
>compilation
>stops at a very initial step and gives out the error:
>
>*checking whether the Fortran compiler (gfortran  ) works... yeschecking
>whether the Fortran compiler (gfortran  ) is a cross-compiler... nochecking
>whether the Fortran compiler (gfortran  ) supports TYPE(*) for
>CCTK_PointerTo... yeschecking how to run the C preprocessor... cppchecking
>for ANSI C header files... nochecking for C99 features... yeschecking for
>M_PI... noconfigure: error: M_PI not defined. Try adding -D_XOPEN_SOURCE to
>CPPFLAGS.*
>
>We tried adding -D_XOPEN_SOURCE to CPPFLAGS, but it does not help. This
>error is consistent if we set up using Intel Compiler (2020 or 2019), or
>gcc (11 or 10). I have attached the outfile, error file, machine script,
>and option lists for both cases (Intel and gcc) for any reference.
>
>Secondly, we are not allowed to compile ETK on login nodes. So we are
>queuing a job script, which upon execution, enters the Cactus directory,
>does "setup-silent", and then executes the build command. Is this the right
>way to compile ETK using the batch script? Or should we do something
>different? I have attached the shell script (compile.sh) used for sbatch
>queue for reference.

I might be wrong, but setup-silent will not use your machine file which
contains all the compiler flags, but will setup something "from scratch"
instead. According to the logs, this will be, e.g., in

/home/shamims.iiserb/ET_debug/Cactus/repos/simfactory2/mdb/machines/cn139.iitr.ac.in.ini

My guess would be that this misses the compiler flags necessary to have
M_PI defined. The best way to get this working might be to let
simfactory also detect the cluster configuration on the compute nodes
(where you compile), such that setup-silent is not needed, but instead
the correct cluster configuration is found and used automatically. In
order to do that, look at examples of 'aliaspattern' in the mdb/machines
directory. An alternative would be to tell simfactory specifically that
you want to use your machine configuration file.

As a side-note: I noticed the command 'patch' is missing too. This is a
tool so common that it should be installed everywhere. Your admin is
probably the best person to ask for advise here. It should not be too
hard to install yourself, but that should not be necessary either,
especially when you are told to compile on compute nodes.

Frank


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